RNA secondary structure prediction with KNetFold

KNetFold Homepage

RNA secondary structure prediction based on machine learning

KNetFold is a software for predicting the consensus RNA secondary structure for a given alignment of nucleotide sequences. You can read about the scientific background of this software in the help document or in our recent publication: Bindewald, E and Shapiro B.A (2006): RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA. 12(3): 342-352 (2006).

This server was developed in the research group of Dr. Bruce A. Shapiro. This server is hosted by the Advanced Biomedical Computing Center (ABCC) of the National Cancer Institute (Frederick Campus).

Quick start

For a really quick start, simply use the form filled with the example tRNA alignment and click "submit". If you want to compute a prediction using your own set of sequences, you need to paste a set aligned RNA sequences (in FASTA format) into the sequence text area of the form below. Providing the email address is currently not possible. Be aware that computing the results can take more than an hour (depending on the length of the submitted alignment). The use of the options is explained in the help text. To obtain old results go to the result retriever page.

Fill text area with example sequences: tRNAtRNA anticodon loop